Before moving on in this discussion, let’s just all try to agree on one simple fact: that nested hierarchies are far more complex and robust than creationists often make them out to be. All three of the major creationist organizations claim that nested hierarchies are merely different levels of similarity between extant organisms. But biological nested hierarchies are much more than this. Biological phylogenies have:
- Nested hierarchy in sequences where function does not change between organisms.
For example, in the OP, I constructed a phylogeny based on CYT B, CYT C, and COX1 proteins. These are all proteins that operate in the electron transport chain, and so they do the exact same thing in all of the taxa from that phylogeny. In fact, life quite literally depends on them doing the exact same thing in every organism; if they did not, then our mitochondria could no longer make ATP.
- Nested hierarchy in unconstrained sequences.
There are certain places in the genome (including functional sequences, so this isn’t a “junk DNA” argument) where changes in sequence do not effect a change in function. For example, at ‘silent sites’ in protein-coding genes, mutations do not affect the protein that is transcribed from the DNA, and many studies have shown that such mutations are functionally neutral. Yet these sites, too, exhibit nested hierarchy, as do other unconstrained sequences like ERVs.
(Note: this is not the same as the “shared ERV” argument, this is referring to the sequences within the ERVs rather than the placement of the ERVs themselves.)
- Ancestral convergence.
We can use ancestral sequence reconstruction (which has been experimentally proven to be highly accurate) to phylogenetically reconstruct ancestral gene sequences for a group of organisms. When we do this on large groups of organisms (for example, comparing all deuterostomes to all protostomes), the ancestral sequences are more similar to one another than the extant sequences, to an insane degree of statistical certainty (p-value: 2.59 x 10^-132). This shows that nested hierarchies are not merely an artifact of similarities of modern organisms, but actually represent divergence in the past.
- Functional ancestral proteins.
Again, ancestral sequence reconstruction has been experimentally shown to be highly accurate. When we conduct ancestral sequence reconstruction on proteins from modern groups of organisms, the resulting ancestral protein sequences are actually functional. This has been done dozens of times, and has been used to reconstruct the evolutionary history (mutation by mutation) of different proteins, for example, hemoglobin. This, like ancestral convergence, shows that nested hierarchies aren’t merely an artifact, but represent real histories of organisms. If a common ancestor didn’t exist, why would its proteins be functional?
If we tried to apply these four features to human-designed objects, like the oft-used ‘vehicle phylogeny,’ it should be obvious that it doesn’t work. Finding nested hierarchy in unconstrained sequences would be like trying to build a phylogeny of vehicles based on features that don’t affect their function, like paint color or the presence of a sunroof. You couldn’t do it, and even if you could, the resulting phylogeny wouldn’t agree with the phylogeny of, for example, engine parts.
Trying to find ancestral convergence in vehicles would be like finding that the ‘bicycle ancestor’ is more similar to the ‘car ancestor’ than extant bicycles and cars are to one another. This would be a meaningless endeavor since vehicles don’t have ancestors anyway, but even if you tried, it would fail since cars have been cars, and bicycles bicycles, as long as they have existed. They never transitioned from bicycles to cars or vice versa. And trying to conduct ancestral sequence reconstruction on vehicles would be like discovering that the ‘ancestor’ of bicycles and cars is a working vehicle – also a meaningless endeavor that is doomed to fail.
For the creationists here, I hope this helps you to see that nested hierarchies are much more robustly supported than the creationist organizations make them out to be, even if you still don’t think that they represent real evolutionary histories.